In silico engineering and optimization of Transcription Activator-Like Effectors and their derivatives for improved DNA binding predictions

الموضوعات

علوم تطبيقية وتكنولوجية

الملخص

Transcription Activator-Like Effectors (TALEs) can be used as adaptable DNA binding modules to create site-specific chimeric nucleases or synthetic transcriptional regulators. The central repeat domain mediates specific DNA bindingvia hypervariable repeat di-residues (RVDs). This DNA-Binding Domain can be engineered to bind preferentially to any user-selected DNA sequence if engineered appropriately. Therefore, TALEs and their derivatives have become indispensable molecular tools in site-specific manipulation of genes and genomes. This thesis revolves around two problems: in silico design and improved bindingsite prediction of TALEs. In the first part, a study is shown where TALEs aresuccessfully designed in silico and validated in laboratory to yield the anticipatedeffects on selected genes. Software is developed to accompany the process ofdesigning and prediction of binding sites. I expanded the functionality of thesoftware to be used as a more generic set of tools for the design, target and offtargetsearching.Part two contributes a method and associated toolkit developed to allow users todesign in silico optimized synthetic TALEs with user-defined specificities for variousexperimental purposes. This method is based on a mutual relationship of three consecutive tandem repeats in the DNA-binding domain. This approach revealedpositional and compositional bias behind the binding of TALEs to DNA.In conclusion, I developed methods, approaches, and software to enhance thefunctionality of synthetic TALEs, which should improve understanding of TALEsbiology and will further advance genome-engineering applications in variousorganisms and cell types.

روابط وملفات

التعريف والنوع

رقم الوثيقة

eeac1824-c2a9-4395-a088-1e3d6481edd2

رقم العقد

0

نوع الوسائط

Crawler

نوع المحتوى

الرسائل العلمية

صيغة المصدر

رسائل دكتوراة

نوع الملف

pdf text

أسماء الملفات

1700026_1.pdf

بيانات النشر

ألقاب المؤلفين

[{"name_ar":"Magdy Mahfouz","title_ar":"اشراف","title_en":"Supervision"},{"name_ar":"Marek Piątek","title_ar":"اعداد","title_en":"Preparation"},{"name_ar":"Vladimir Bajic","title_ar":"اشراف","title_en":"Supervision"}]

اللغة

English

المصدر والدورية

اسم المصدر

In silico engineering and optimization of Transcription Activator-Like Effectors and their derivatives for improved DNA binding predictions

المحتوى والصفحات

عدد الصفحات

0

كلمات الباحثين

Bioinformatics , Genome engineering , TALE binding code , TALE target prediction , Transcription Activator-Like Effector

إشراف وإعداد

الإشراف

Magdy Mahfouz, Vladimir Bajic

الإعداد

Marek Piątek

الاقتباسات الببليوغرافية